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Merge remote-tracking branch 'upstream/master' into jdk9
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* upstream/master: (229 commits)
  Try to fix not on FX thread for search and autocomplete (#4618)
  Convert DuplicateResolverDialog to javafx (#4601)
  Fix for BibTex source tab parsing issue if field contains {} (#4581)
  Convert OO/LO SidePanel to javafx (#4341)
  Convert "Customize importer" dialog to JavaFX (#4608)
  Convert "From Aux file" dialog to JavaFX (#4607)
  Convert "Show preferences" dialog to JavaFX (#4605)
  Fix not on FX thread exception
  Force javafx to run thread (#4604)
  Convert new version dialog to JavaFX (#4602)
  Add a variable to track the change in preview style (#4587)
  Solution for submitting dialog with Ctrl + Enter (#4496) (#4592)
  Bump mysql-connector-java from 8.0.13 to 8.0.14 (#4599)
  Fix overlapping font in id entry type (#4595)
  update jfoenix and gradle plugins Replace outdated transformer log4j2 with official new one
  Update journalList.txt
  Fix for Issue #4437 - Some bugs in preference->Entry table columns (#4546)
  Don't set column sort type at startup (#4577)
  Add uncaught exception message (#4565)
  Converts integrity check dialog to JavaFX (#4559)
  ...

# Conflicts:
#	build.gradle
#	src/main/java/org/jabref/gui/FindUnlinkedFilesDialog.java
#	src/main/java/org/jabref/gui/JabRefFrame.java
#	src/main/java/org/jabref/gui/fieldeditors/EditorTextArea.java
#	src/main/java/org/jabref/gui/fieldeditors/EditorTextField.java
#	src/main/java/org/jabref/gui/openoffice/CitationManager.java
#	src/main/java/org/jabref/gui/openoffice/OOBibBase.java
#	src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
#	src/main/java/org/jabref/gui/openoffice/OpenOfficeSidePanel.java
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Siedlerchr committed Jan 27, 2019
2 parents 85f9685 + 69661a4 commit 0a54822
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85 changes: 85 additions & 0 deletions .circleci/config.yml
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version: 2

jobs:
downloadinstall4j:
docker:
- image: circleci/openjdk:8-jdk
steps:
- checkout
- run: git submodule sync
- run: git submodule update --init
- restore_cache:
keys:
- install4j-{{ checksum "scripts/extract-install4j.sh" }}
- run: scripts/download-install4j-and-jres.sh
- save_cache:
key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
paths:
- "~/downloads"
- "~/.install4j7"
filters:
tags:
only: /.*/

buildDev:
docker:
- image: circleci/openjdk:8-jdk
steps:
- restore_cache:
key: dependency-cache
- checkout
- run: git submodule sync
- run: git submodule update --init
- restore_cache:
key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
- run: scripts/extract-install4j.sh
- run: install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY
- run: ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
- save_cache:
key: dependency-cache
paths:
- "~/.gradle"
- store_artifacts:
path: build/releases
destination: build
- run: scripts/upload-to-builds.jabref.org.sh

buildRelease:
docker:
- image: circleci/openjdk:8-jdk
steps:
- restore_cache:
key: dependency-cache
- checkout
- run: git submodule sync
- run: git submodule update --init
- restore_cache:
key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
- run: scripts/extract-install4j.sh
- run: install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY
- run: ./gradlew -Pinstall4jDir="install4j7" release --stacktrace
- store_artifacts:
path: build/releases
destination: release
- run: scripts/upload-to-builds.jabref.org.sh
filters:
tags:
only: /.*/

workflows:
version: 2
build:
jobs:
- downloadinstall4j
- buildDev:
requires:
- downloadinstall4j
- buildRelease:
requires:
- downloadinstall4j
filters:
branches:
ignore: /.*/
tags:
only: /.*/

26 changes: 0 additions & 26 deletions .github/ISSUE_TEMPLATE.md

This file was deleted.

40 changes: 40 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.md
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---
name: Bug report
about: Create a report to help us improve

---

<!--
Note: Please use the GitHub issue tracker only for bug reports.
Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
Thanks!
-->

JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubuntu 14.04|Mac OS X 10.8|... -->

<!-- IMPORTANT NOTE ->
<!--
Please always test if the bug is still reproducible in the latest development version.
We are constantly improving JabRef and some bugs may already be fixed.
You can download the development version at: http://builds.jabref.org/master/
Please make a backup of your library before you try out this version.
If you already use a development version, ensure that you use the latest one.
-->
- [ ] I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists

<!-- Add a clear and concise description of what the bug is. -->

Steps to reproduce the behavior:
1. ...
2. ...
3. ...

<!-- If applicable, add excerpt of the bibliography file, screenshot, and excerpt of log (available in the error console) -->

<details>
<summary>Log File</summary>

```
Paste an excerpt of your log file here
```
</details>
9 changes: 9 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md
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---
name: Feature request
about: Suggest an idea for this project

---

Please use the GitHub issue tracker only for bug reports and suggestions for improvements.
Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
Thanks!
9 changes: 9 additions & 0 deletions .github/ISSUE_TEMPLATE/question.md
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@@ -0,0 +1,9 @@
---
name: Question
about: Ask a question about JabRef

---

Please use the GitHub issue tracker only for bug reports and suggestions for improvements.
Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
Thanks!
20 changes: 20 additions & 0 deletions .github/ISSUE_TEMPLATE/suggestion-for-improvement.md
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---
name: Suggestion for improvement
about: Suggest an enhancement

---

<!--
Please use the GitHub issue tracker only for bug reports and smaller suggestions for improvements.
Requests for completely new features, questions and general feedback is now handled at http://discourse.jabref.org.
Thanks!
-->

**Is your suggestion for improvement related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]

**Describe the solution you'd like**
A clear and concise description of what you want to happen.

**Additional context**
Add any other context or screenshots about the feature request here.
6 changes: 6 additions & 0 deletions .gitmodules
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[submodule "src/main/resources/csl-styles"]
path = src/main/resources/csl-styles
url = https://github.com/citation-style-language/styles.git
[submodule "src/main/resources/csl-locales"]
path = src/main/resources/csl-locales
url = https://github.com/citation-style-language/locales.git
3 changes: 2 additions & 1 deletion .travis.yml
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Expand Up @@ -48,7 +48,7 @@ before_script:
script:
# --scan enables the Gradle build scan, which can be used to investigate the time each action consumes
# For more information see https://gradle.com/scans/get-started
- if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS --scan; fi
- if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS -x checkstyleJmh -x checkstyleMain -x checkstyleTest --scan; fi
- if [ "$TEST_SUITE" == "checkstyle" ]; then ./gradlew checkstyleMain checkstyleTest checkstyleJmh; fi
- if [ "$TEST_SUITE" == "guiTest" ]; then ./buildres/gui-tests.sh; fi
- if [ "$TEST_SUITE" == "codecov" ]; then ./gradlew jacocoTestReport; bash <(curl -s https://codecov.io/bash); fi
Expand All @@ -72,3 +72,4 @@ cache:
directories:
- $HOME/.gradle/caches/
- $HOME/.gradle/wrapper/

1 change: 1 addition & 0 deletions AUTHORS
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@ Alexsandro Lauber
Ali Ayan
Alick Zhao
Ambrogio Oliva
Amish Shah
Andreas Amann
Andreas Buhr
Andreas Rudert
Expand Down
53 changes: 42 additions & 11 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,19 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
## [Unreleased]

### Changed
- We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
- Journal/Year/Month in biblatex mode -> Deprecated (if filled)
- DOI/URL: General -> Optional
- Internal fields like ranking, read status and priority: Other -> General
- Moreover, empty deprecated fields are no longer shown
- Added server timezone parameter when connecting to a shared database.
- We updated the dialog for setting up general fields.
- URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
- We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
- We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
- Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
- We added a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field.
Because of this change, the last-used cleanup operations were reset.
- We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works. [4093](https://github.com/JabRef/jabref/issues/4093)
- The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
- We added a button in the tab header which allows you to close the database with one click. https://github.com/JabRef/jabref/issues/494
Expand All @@ -25,14 +36,27 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
- We changed the default keyboard shortcuts for moving between entries when the entry editor is active to ̀<kbd>alt</kbd> + <kbd>up/down</kbd>.
- Opening a new file now prompts the directory of the currently selected file, instead of the directory of the last opened file.
- Window state is saved on close and restored on start.
- We made the MathSciNet fetcher more reliable.
- We added the ISBN fetcher to the list of fetcher available under "Update with bibliographic information from the web" in the entry editor toolbar.
- Files without a defined external file type are now directly opened with the default application of the operating system
- We streamlined the process to rename and move files by removing the confirmation dialogs.


- We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
- We add auto url formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
- We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
- We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl</kbd> + <kbd>E</kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
- We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
- We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
- We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
- We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
- We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
- We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
- We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)




### Fixed
- We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
- We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
- Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
- The entry editor no longer gets corrupted after using the source tab. https://github.com/JabRef/jabref/issues/3532 https://github.com/JabRef/jabref/issues/3608 https://github.com/JabRef/jabref/issues/3616
Expand All @@ -47,9 +71,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
- We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
- We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
- We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. https://github.com/JabRef/jabref/issues/3146
- We improved the integrity check for page numbers. [#4113](https://github.com/JabRef/jabref/issues/4113) and [feature request in the forum](http://discourse.jabref.org/t/pages-field-allow-use-of-en-dash/1199)
- We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
- We fixed an issue where renaming a group did not change the group name in the interface. [#3189](https://github.com/JabRef/jabref/issues/3189)
- We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
- We fixed an issue where the "Open file dialog" may disappear behind other windows. https://github.com/JabRef/jabref/issues/3410
- We fixed an issue where the number of entries matched was not updated correctly upon adding or removing an entry. [#3537](https://github.com/JabRef/jabref/issues/3537)
- We fixed an issue where the default icon of a group was not colored correctly.
- We fixed an issue where the first field in entry editor was not focused when adding a new entry. [#4024](https://github.com/JabRef/jabref/issues/4024)
- We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files https://github.com/JabRef/jabref/issues/2970
Expand All @@ -58,12 +85,14 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
- We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
- We fixed an issue where the preview pane in entry preview in preferences wasn't showing the citation style selected [#3849](https://github.com/JabRef/jabref/issues/3849)
- We fixed an issue where the default entry preview style still contained the field `review`. The field `review` in the style is now replaced with comment to be consistent with the entry editor [#4098](https://github.com/JabRef/jabref/issues/4098)






- We fixed an issue where users were vulnerable to XXE attacks during parsing [#4229](https://github.com/JabRef/jabref/issues/4229)
- We fixed an issue where files added via the "Attach file" contextmenu of an entry were not made relative. [#4201](https://github.com/JabRef/jabref/issues/4201) and [#4241](https://github.com/JabRef/jabref/issues/4241)
- We fixed an issue where author list parser can't generate bibtex for Chinese author. [#4169](https://github.com/JabRef/jabref/issues/4169)
- We fixed an issue where the list of XMP Exclusion fields in the preferences was not be saved [#4072](https://github.com/JabRef/jabref/issues/4072)
- We fixed an issue where the ArXiv Fetcher did not support HTTP URLs [koppor#328](https://github.com/koppor/jabref/issues/328)
- We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
- We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
- We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)



Expand All @@ -79,6 +108,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
- Set/clear/append/rename fields: available through Edit menu
- Manage keywords: available through Edit menu
- Copy linked files to folder: available through File menu
- We removed the option to change the column widths in the preferences dialog. [#4546](https://github.com/JabRef/jabref/issues/4546)



Expand Down Expand Up @@ -111,9 +141,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#

## Older versions

The changelog of JabRef 4.x is available at the [v4.x branch](https://github.com/JabRef/jabref/blob/v4.x/CHANGELOG.md).
The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
The changelog of JabRef 4.x is available at the [v4.x branch](https://github.com/JabRef/jabref/blob/v4.x/CHANGELOG.md).
The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).

[Unreleased]: https://github.com/JabRef/jabref/compare/v4.3...HEAD
[4.3]: https://github.com/JabRef/jabref/compare/v4.2...v4.3
Expand All @@ -125,3 +155,4 @@ The changelog of JabRef 2.11 and all previous versions is available as [text fil
[4.0-beta]: https://github.com/JabRef/jabref/compare/v3.8.2...v4.0-beta
[2.11.1]: https://github.com/JabRef/jabref/compare/v2.11...v2.11.1
[JavaFX]: https://en.wikipedia.org/wiki/JavaFX

4 changes: 1 addition & 3 deletions README.md
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Expand Up @@ -101,9 +101,7 @@ When you want to develop, it is necessary to generate additional sources using `
and then generate the Eclipse `gradlew eclipse`.
For IntelliJ IDEA, just import the project via a Gradle Import by pointing at the `build.gradle`.

`gradlew test` executes the normal unit tests.
If you want to test the UI, execute `gradlew integrationTest`.
Sources for the integration test are kept in `src/integrationTest`.
`gradlew test` executes all tests. We use [Travis CI](https://travis-ci.org/) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Travis will report any other failure.


## Acknowledgements
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